diff --git a/src/query_builder/cypher_builder.rs b/src/query_builder/cypher_builder.rs index 1e14479..52bff6d 100644 --- a/src/query_builder/cypher_builder.rs +++ b/src/query_builder/cypher_builder.rs @@ -164,7 +164,7 @@ pub async fn query_nhops( } // Parse the shared nodes and edges from the result. -// NOTE: the name of the results should be 'common', 'relatedStartNodes', and 'relations'. +// NOTE: the name of the results should be 'common', 'relatedNodes', and 'relations'. // // # Arguments // * `result` - The result of the query. @@ -186,10 +186,10 @@ async fn parse_shared_results( let node = NodeData::from_neo_node(node); node_map.insert(id, node); } - None => continue, + None => (), }; - match row.get::>("relatedStartNodes") { + match row.get::>("relatedNodes") { Some(related_start_nodes) => { for node in related_start_nodes { let id = node.id(); @@ -197,7 +197,16 @@ async fn parse_shared_results( node_map.insert(id, node); } } - None => continue, + None => (), + }; + + match row.get::("startNode") { + Some(node) => { + let id = node.id(); + let node = NodeData::from_neo_node(node); + node_map.insert(id, node); + } + None => (), }; // If you want to know the format of the relations, you can run the related cypher query in the Neo4j Browser. @@ -209,9 +218,29 @@ async fn parse_shared_results( } } } - None => continue, + None => (), + }; + + match row.get::>("relations1") { + Some(relation) => { + for r in relation { + relations.push(r); + } + } + None => (), + }; + + match row.get::>("relations2") { + Some(relation) => { + for r in relation { + relations.push(r); + } + } + None => (), }; } + info!("Number of entities: {}", &node_map.len()); + info!("Number of relations: {}", &relations.len()); for relation in relations.iter() { let start_node_id = relation.start_node_id(); @@ -251,27 +280,14 @@ pub async fn query_shared_nodes( nums_shared_by: usize, start_node_id: Option<&str>, ) -> Result<(Vec, Vec), anyhow::Error> { - let nums_shared_by = if nums_shared_by == 0 || nums_shared_by > node_ids.len() { - node_ids.len() - } else { - nums_shared_by - }; - - let where_clauses = match target_node_types { - Some(target_node_types) => { - format!( - "sharedBy = {} AND ANY(label IN labels(common) WHERE label IN ['{}'])", - nums_shared_by, - target_node_types.join("', '") - ) - } - None => format!("sharedBy = {}", nums_shared_by), + if nums_shared_by > node_ids.len() { + return Err(anyhow::anyhow!( + "The number of shared nodes should be less than the number of start nodes." + )); }; - let hop_str = match nhops { - 1 => "*1", - 2 => "*1..2", - _ => "", + if nhops > 2 { + return Err(anyhow::anyhow!("The number of hops should be less than 3.")); }; let query_str = if start_node_id.is_none() { @@ -283,9 +299,9 @@ pub async fn query_shared_nodes( // UNWIND startNodes AS startNode // MATCH p=(startNode)-[r*1]-(common:Disease) // WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN startNodes OR x = common) - // WITH common, COLLECT(DISTINCT startNode) AS relatedStartNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy + // WITH common, COLLECT(DISTINCT startNode) AS relatedNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy // WHERE sharedBy = 2 - // RETURN common, relatedStartNodes, relations + // RETURN common, relatedNodes, relations // ORDER BY sharedBy DESC // LIMIT 100 @@ -297,28 +313,65 @@ pub async fn query_shared_nodes( if i < node_ids.len() - 1 { start_nodes_details.push_str(", "); } + } + let nums_shared_by = if nums_shared_by == 0 || nums_shared_by > node_ids.len() { + node_ids.len() + } else { + nums_shared_by }; - format!(" - WITH [{start_nodes_details}] AS startNodesDetails - UNWIND startNodesDetails AS nodeDetails - MATCH (start) - WHERE start.id = nodeDetails.id AND ANY(label IN labels(start) WHERE label = nodeDetails.label) - WITH COLLECT(DISTINCT start) AS startNodes - UNWIND startNodes AS startNode - MATCH p=(startNode)-[r{hop_str}]-(common) - WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN startNodes OR x = common) AND startNode IN startNodes - WITH common, COLLECT(DISTINCT startNode) AS relatedStartNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy - WHERE {where_clauses} - WITH common, relatedStartNodes, relations, sharedBy - ORDER BY sharedBy DESC - LIMIT {topk} - RETURN common, relatedStartNodes, relations", - topk = topk, - start_nodes_details = start_nodes_details, - hop_str = hop_str, - where_clauses = where_clauses - ) + let where_clauses = match target_node_types { + Some(target_node_types) => { + format!( + "sharedBy = {} AND ANY(label IN labels(common) WHERE label IN ['{}'])", + nums_shared_by, + target_node_types.join("', '") + ) + } + None => format!("sharedBy = {}", nums_shared_by), + }; + + if nhops == 1 { + format!(" + WITH [{start_nodes_details}] AS startNodesDetails + UNWIND startNodesDetails AS nodeDetails + MATCH (start) + WHERE start.id = nodeDetails.id AND ANY(label IN labels(start) WHERE label = nodeDetails.label) + WITH COLLECT(DISTINCT start) AS startNodes + UNWIND startNodes AS startNode + MATCH p=(startNode)-[r]-(common) + WHERE (NOT startNode = common) AND ALL(x IN nodes(p) WHERE x IN startNodes) AND startNode IN startNodes + WITH common, COLLECT(DISTINCT startNode) AS relatedNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy + WHERE {where_clauses} + WITH common, relatedNodes, relations, sharedBy + ORDER BY sharedBy DESC + LIMIT {topk} + RETURN common, relatedNodes, relations", + topk = topk, + start_nodes_details = start_nodes_details, + where_clauses = where_clauses + ) + } else { + format!(" + WITH [{start_nodes_details}] AS startNodesDetails + UNWIND startNodesDetails AS nodeDetails + MATCH (start) + WHERE start.id = nodeDetails.id AND ANY(label IN labels(start) WHERE label = nodeDetails.label) + WITH COLLECT(DISTINCT start) AS startNodes + UNWIND startNodes AS startNode + MATCH p=(startNode)-[r*1..2]-(common) + WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN startNodes OR x = common) AND startNode IN startNodes + WITH common, COLLECT(DISTINCT startNode) AS relatedNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy + WHERE {where_clauses} + WITH common, relatedNodes, relations, sharedBy + ORDER BY sharedBy DESC + LIMIT {topk} + RETURN common, relatedNodes, relations", + topk = topk, + start_nodes_details = start_nodes_details, + where_clauses = where_clauses + ) + } } else { let start_node_id = start_node_id.unwrap(); let (start_node_label, start_node_id) = split_id(start_node_id)?; @@ -332,32 +385,81 @@ pub async fn query_shared_nodes( .collect::>() .join(", "); - format!(" - // 假设 start_node_id 和 start_node_label 代表我们感兴趣的起始节点的ID和标签 - MATCH (start) - WHERE start.id = '{start_node_id}' AND ANY(label IN labels(start) WHERE label = '{start_node_label}') - WITH start AS startNode - // 这里不再需要收集起始节点，因为我们只有一个起始节点 - UNWIND [{other_nodes_details}] AS otherNodeDetails - MATCH (other) - WHERE other.id = otherNodeDetails.id AND ANY(label IN labels(other) WHERE label = otherNodeDetails.label) - WITH COLLECT(DISTINCT other) AS otherNodes, startNode - UNWIND otherNodes AS otherNode - MATCH p=(startNode)-[r{hop_str}]-(common) - WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN otherNodes OR x = common) AND startNode = startNode - WITH common, COLLECT(DISTINCT otherNode) AS relatedOtherNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT otherNode) AS sharedBy - WHERE {where_clauses} - WITH common, relatedOtherNodes, relations, sharedBy - ORDER BY sharedBy DESC - LIMIT {topk} - RETURN common, relatedOtherNodes, relations", - topk = topk, - other_nodes_details = other_nodes_details, // 该变量需要提供其他节点的详情，例如ID和标签 - hop_str = hop_str, - where_clauses = where_clauses, - start_node_id = start_node_id, // 指定的起始节点ID - start_node_label = start_node_label // 指定的起始节点标签 - ) + if nhops == 1 { + format!(" + MATCH (start) + WHERE start.id = '{start_node_id}' AND ANY(label IN labels(start) WHERE label = '{start_node_label}') + WITH start AS startNode + UNWIND [{other_nodes_details}] AS otherNodeDetails + MATCH (other) + WHERE other.id = otherNodeDetails.id AND ANY(label IN labels(other) WHERE label = otherNodeDetails.label) + WITH COLLECT(DISTINCT other) AS otherNodes, startNode + UNWIND otherNodes AS otherNode + MATCH (startNode)-[r]-(sharedNode) + WHERE sharedNode = otherNode + WITH sharedNode, COLLECT(r) AS relations1, startNode, COLLECT(DISTINCT otherNode) AS relatedNodes + RETURN sharedNode AS common, relations1, relatedNodes, startNode", + other_nodes_details = other_nodes_details, + start_node_id = start_node_id, + start_node_label = start_node_label + ) + } else { + let where_clauses = match target_node_types { + Some(target_node_types) => { + format!( + "sharedBy = {} AND ANY(label IN labels(common) WHERE label IN ['{}'])", + nums_shared_by, + target_node_types.join("', '") + ) + } + None => format!("sharedBy = {}", nums_shared_by), + }; + + // Example query string: + // MATCH (startNode) + // WHERE startNode.id = 'ENTREZ:3569' AND ANY(label IN labels(startNode) WHERE label = 'Gene') + // WITH startNode + // UNWIND [{label: 'Gene', id: 'ENTREZ:3107'}, {label: 'Gene', id: 'ENTREZ:3119'}, {label: 'Gene', id: 'ENTREZ:3569'}] AS otherNodeDetail + // MATCH (otherNode) + // WHERE otherNode.id = otherNodeDetail.id AND ANY(label IN labels(otherNode) WHERE label = otherNodeDetail.label) + // WITH COLLECT(DISTINCT otherNode) AS otherNodes, startNode + // MATCH (startNode)-[r1]-(sharedNode) + // WHERE NOT (sharedNode IN otherNodes) + // WITH sharedNode, COLLECT(DISTINCT r1) AS relations, startNode, otherNodes + // MATCH (sharedNode)-[r2]-(otherNode) + // WHERE otherNode IN otherNodes AND otherNode <> startNode + // WITH sharedNode, relations, startNode, COLLECT(DISTINCT otherNode) AS relatedNodes, COLLECT(DISTINCT r2) AS relations2, COUNT(DISTINCT otherNode) AS sharedBy + // WHERE sharedBy = 2 AND ANY(label IN labels(sharedNode) WHERE label IN ['Gene']) + // WITH sharedNode AS common, relations AS relations1, relatedNodes, startNode, relations2, sharedBy + // ORDER BY sharedBy DESC + // LIMIT 3 + // RETURN common, relations1, relatedNodes, startNode, relations2 + format!(" + MATCH (startNode) + WHERE startNode.id = '{start_node_id}' AND ANY(label IN labels(startNode) WHERE label = '{start_node_label}') + WITH startNode + UNWIND [{other_nodes_details}] AS otherNodeDetail + MATCH (otherNode) + WHERE otherNode.id = otherNodeDetail.id AND ANY(label IN labels(otherNode) WHERE label = otherNodeDetail.label) + WITH COLLECT(DISTINCT otherNode) AS otherNodes, startNode + MATCH (startNode)-[r1]-(sharedNode) + WHERE NOT (sharedNode IN otherNodes) + WITH sharedNode, COLLECT(DISTINCT r1) AS relations, startNode, otherNodes + MATCH (sharedNode)-[r2]-(otherNode) + WHERE otherNode IN otherNodes AND otherNode <> startNode + WITH sharedNode AS common, relations, startNode, COLLECT(DISTINCT otherNode) AS relatedNodes, COLLECT(DISTINCT r2) AS relations2, COUNT(DISTINCT otherNode) AS sharedBy + WHERE {where_clauses} + WITH common, relations AS relations1, relatedNodes, startNode, relations2, sharedBy + ORDER BY sharedBy DESC + LIMIT {topk} + RETURN common, relations1, relatedNodes, startNode, relations2", + other_nodes_details = other_nodes_details, + where_clauses = where_clauses, + start_node_id = start_node_id, + start_node_label = start_node_label, + topk = topk + ) + } }; info!("query_shared_nodes's query_str: {}", query_str); diff --git a/studio/package.json b/studio/package.json index 2f1f356..c05f446 100644 --- a/studio/package.json +++ b/studio/package.json @@ -31,7 +31,7 @@ "antd": "5.7.0", "antd-schema-form": "^4.5.1", "axios": "^1.1.2", - "biominer-components": "0.2.77", + "biominer-components": "0.2.78", "classnames": "^2.3.0", "handlebars": "^4.7.7", "handsontable": "^12.1.3", diff --git a/studio/yarn.lock b/studio/yarn.lock index bc69ce2..5b1851d 100644 --- a/studio/yarn.lock +++ b/studio/yarn.lock @@ -5772,10 +5772,10 @@ bindings@^1.5.0: dependencies: file-uri-to-path "1.0.0" -biominer-components@0.2.77: - version "0.2.77" - resolved "https://registry.yarnpkg.com/biominer-components/-/biominer-components-0.2.77.tgz#ec89d0463140993509a7eb20f876d1bc8428bba4" - integrity sha512-RqE19JGB9J12dXm6l6Q16nVxU1pLeFI+9FC70hXRFYSYSaYkJnGlRWy/qjn7KWRsWiJXGA4hZjmfAdVzM1mI5g== +biominer-components@0.2.78: + version "0.2.78" + resolved "https://registry.yarnpkg.com/biominer-components/-/biominer-components-0.2.78.tgz#d74e8c4bbe29e48d349242fb5d7f3875593deef4" + integrity sha512-xOyatggnwtzLDbMxM8kzksFvhM5VzU195RuLG8ixXjdYT1HKZRpphv2wA1PVjju3at6FlLhon4JYOkz3eF7e3Q== dependencies: "@fingerprintjs/fingerprintjs" "^3.4.2" "@types/openseadragon" "^3.0.3"